A new balancing algorithm for double star capacitor bank based on targeting function is proposed in this paper. Firstly, the target center-point is determined by the targeting function, and then the shooting function is used to perform full-coverage and accurate shoot-processing in each round. According to the preset standard unbalance ratio, an optimal set of balancing strategies is finally calculated to achieve the purpose of balance of the double star capacitor bank. Practical program based on the balancing algorithm is formed and applied to practice,which achieves good results and the effectiveness and practical value of the algorithm is verified. This algorithm has the advantages of small amount of calculation, fast convergence and optimal substitution strategy, and has good application prospect and promotion value.